Detailed imaging of pulmonary artery (PA) anatomy and significant aorto-pulmonary collaterals (APCs) is crucial for surgical planning and follow-up in patients with complex congenital heart disease (CHD) and pulmonary stenosis or atresia. Because examination by echocardiography is often technically limited and catheterization is invasive, this study evaluated the diagnostic accuracy of magnetic resonance imaging (MRI) as an alternate non-invasive tool. Thirteen patients (median age 28 years, range: 1-44 years) underwent both cardiac catheterization and MRI within a median of two months (range 0.1-8 months). Diagnoses included tetralogy of Fallot (TOF) with pulmonary atresia (n = 8), TOF with pulmonary stenosis (n = 2), single left ventricle with pulmonary stenosis (n = 2), and complex heterotaxy with pulmonary stenosis (n = 1). The MRI sequences used in this study were ECG-gated spin echo and gradient echo sequences acquired in multiple planes. Compared to catheterization, MRI had 100% sensitivity and specificity for the diagnosis of main PA (n = 6) and branch PA (n = 13) hypoplasia or stenosis, as well as discontinuous (n = 4) or absent (n = 10) branch PAs. There was complete agreement between catheterization and MRI identification of significant APCs (n = 18). Main PA atresia was noted by MRI in four patients but was not definitively seen by catheterization in any. MRI but not catheterization precisely defined the distance between discontinuous PAs and their relationship to other mediastinal structures. In conclusion, cardiac MRI is a reliable non-invasive imaging modality to define PA and APC anatomy in patients with complex pulmonary stenosis or atresia.